C. R. Clapier and B. R. Cairns, The biology of chromatin remodeling complexes, Annu Rev Biochem, vol.78, pp.273-304, 2009.

A. Ramaswamy and I. Ioshikhes, Dynamics of modeled oligonucleosomes and the role of histone variant proteins in nucleosome organization, Adv Protein Chem Struct Biol, vol.90, pp.119-168, 2013.

M. M. Suzuki and A. Bird, DNA methylation landscapes: provocative insights from epigenomics, Nat Rev Genet, vol.9, pp.465-76, 2008.
DOI : 10.1038/nrg2341

S. B. Rothbart and B. D. Strahl, Interpreting the language of histone and DNA modifications, Biochim Biophys Acta, vol.1839, pp.627-670, 2014.

F. Roudier, I. Ahmed, C. Berard, A. Sarazin, T. Mary-huard et al., Integrative epigenomic mapping defines four main chromatin states in Arabidopsis, EMBO J, vol.30, pp.1928-1966, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00999846

J. Sequeira-mendes, I. Araguez, R. Peiro, R. Mendez-giraldez, X. Zhang et al., The functional topography of the Arabidopsis genome is organized in a reduced number of linear motifs of chromatin states, Plant Cell, vol.26, pp.2351-66, 2014.

Z. Vergara and C. Gutierrez, Emerging roles of chromatin in the maintenance of genome organization and function in plants, Genome Biol, vol.18, p.96, 2017.

F. X. Chen, E. R. Smith, and A. Shilatifard, Born to run: control of transcription elongation by RNA polymerase II, Nat Rev Mol Cell Biol, vol.19, pp.464-78, 2018.

Y. Zhou, F. J. Romero-campero, A. Gomez-zambrano, F. Turck, and M. Calonje, H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity, Genome Biol, vol.18, p.69, 2017.

Z. W. Sun and C. D. Allis, Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast, Nature, vol.418, pp.104-112, 2002.

J. Kim, M. Guermah, R. K. Mcginty, J. S. Lee, Z. Tang et al., RAD6-mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells, Cell, vol.137, pp.459-71, 2009.

A. Shilatifard, The COMPASS family of histone H3K4 methylases: mechanisms of regulation in development and disease pathogenesis, Annu Rev Biochem, vol.81, pp.65-95, 2012.

B. Schuettengruber, H. M. Bourbon, D. Croce, L. Cavalli, and G. , Genome regulation by Polycomb and Trithorax: 70 years and counting, Cell, vol.171, pp.34-57, 2017.
DOI : 10.1016/j.cell.2017.08.002

URL : https://hal.archives-ouvertes.fr/hal-01596016

J. S. Lee, A. Shukla, J. Schneider, S. K. Swanson, M. P. Washburn et al., Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS, Cell, vol.131, pp.1084-96, 2007.
DOI : 10.1016/j.cell.2007.09.046

URL : https://doi.org/10.1016/j.cell.2007.09.046

S. Zheng, J. J. Wyrick, and J. C. Reese, Novel trans-tail regulation of H2B ubiquitylation and H3K4 methylation by the N terminus of histone H2A, Mol Cell Biol, vol.30, pp.3635-3680, 2010.

L. M. Soares and S. Buratowski, Yeast Swd2 is essential because of antagonism between Set1 histone methyltransferase complex and APT (associated with Pta1) termination factor, J Biol Chem, vol.287, pp.15219-15250, 2012.
DOI : 10.1074/jbc.m112.341412

URL : http://www.jbc.org/content/287/19/15219.full.pdf

J. L. Thornton, G. H. Westfield, Y. H. Takahashi, M. Cook, X. Gao et al., Context dependency of Set1/COMPASSmediated histone H3 Lys4 trimethylation, Genes Dev, vol.28, pp.115-135, 2014.
DOI : 10.1101/gad.232215.113

URL : http://genesdev.cshlp.org/content/28/2/115.full.pdf

A. Roguev, D. Schaft, A. Shevchenko, W. W. Pijnappel, M. Wilm et al., The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone 3 lysine 4, EMBO J, vol.20, pp.7137-7185, 2001.
DOI : 10.1093/emboj/20.24.7137

URL : http://emboj.embopress.org/content/20/24/7137.full.pdf

T. Miller, N. J. Krogan, J. Dover, H. Erdjument-bromage, P. Tempst et al., COMPASS: a complex of proteins associated with a trithorax-related SET domain protein, Proc Natl Acad Sci U S A, vol.98, pp.12902-12909, 2001.

S. D. Briggs, M. Bryk, B. D. Strahl, W. L. Cheung, J. K. Davie et al., Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae, Genes Dev, vol.15, pp.3286-95, 2001.

P. L. Nagy, J. Griesenbeck, R. D. Kornberg, and M. L. Cleary, A trithorax-group complex purified from Saccharomyces cerevisiae is required for methylation of histone H3, Proc Natl Acad Sci, vol.99, pp.90-94, 2002.

T. Thorstensen, P. E. Grini, and R. B. Aalen, SET domain proteins in plant development, Biochim Biophys Acta, vol.1809, pp.407-427, 2011.
DOI : 10.1016/j.bbagrm.2011.05.008

H. Santos-rosa, R. Schneider, A. J. Bannister, J. Sherriff, B. E. Bernstein et al., Active genes are tri-methylated at K4 of histone H3, Nature, vol.419, pp.407-418, 2002.
DOI : 10.1038/nature01080

H. H. Ng, F. Robert, R. A. Young, and K. Struhl, Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity, Mol Cell, vol.11, pp.709-728, 2003.

R. Schneider, A. J. Bannister, F. A. Myers, A. W. Thorne, C. Crane-robinson et al., Histone H3 lysine 4 methylation patterns in higher eukaryotic genes, Nat Cell Biol, vol.6, pp.73-80, 2004.
DOI : 10.1038/ncb1076

D. Schubeler, D. M. Macalpine, D. Scalzo, C. Wirbelauer, C. Kooperberg et al., The histone modification pattern of active genes revealed through genomewide chromatin analysis of a higher eukaryote, Genes Dev, vol.18, pp.1263-71, 2004.

D. K. Pokholok, C. T. Harbison, S. Levine, M. Cole, N. M. Hannett et al., Genome-wide map of nucleosome acetylation and methylation in yeast, Cell, vol.122, pp.517-544, 2005.

X. Zhang, Y. V. Bernatavichute, S. Cokus, M. Pellegrini, and S. E. Jacobsen, Genomewide analysis of mono-, di-and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana, Genome Biol, vol.10, p.62, 2009.

L. O. Baumbusch, T. Thorstensen, V. Krauss, A. Fischer, K. Naumann et al., The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes, Nucleic Acids Res, vol.29, pp.4319-4352, 2001.

N. M. Springer, C. A. Napoli, D. A. Selinger, R. Pandey, K. C. Cone et al., Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots, Plant Physiol, vol.132, pp.907-932, 2003.

L. Zhang and H. Ma, Complex evolutionary history and diverse domain organization of SET proteins suggest divergent regulatory interactions, New Phytol, vol.195, pp.248-63, 2012.
DOI : 10.1111/j.1469-8137.2012.04143.x

URL : https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2012.04143.x

R. Alvarez-venegas, S. Pien, M. Sadder, X. Witmer, U. Grossniklaus et al., ATX-1, an Arabidopsis homolog of trithorax, activates flower homeotic genes, Curr Biol, vol.13, pp.627-664, 2003.

Y. Tamada, J. Y. Yun, S. C. Woo, and R. M. Amasino, ARABIDOPSIS TRITHORAX-RELATED7 is required for methylation of lysine 4 of histone H3 and for transcriptional activation of FLOWERING LOCUS C, Plant Cell, vol.21, pp.3257-69, 2009.

A. Berr, L. Xu, J. Gao, V. Cognat, A. Steinmetz et al., SET DOMAIN GROUP25 encodes a histone methyltransferase and is involved in FLOWERING LOCUS C activation and repression of flowering, Plant Physiol, vol.151, pp.1476-85, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00430649

A. Berr, E. J. Mccallum, R. Menard, D. Meyer, J. Fuchs et al., Arabidopsis SET DOMAIN GROUP2 is required for H3K4 trimethylation and is crucial for both sporophyte and gametophyte development, Plant Cell, vol.22, pp.3232-3280, 2010.
DOI : 10.1105/tpc.110.079962

URL : https://hal.archives-ouvertes.fr/hal-00539767

L. Guo, Y. Yu, J. A. Law, and X. Zhang, SET DOMAIN GROUP2 is the major histone H3 lysine, Proc Natl Acad Sci, vol.107, pp.18557-62, 2010.
DOI : 10.1073/pnas.1010478107

URL : http://www.pnas.org/content/pnas/107/43/18557.full.pdf

Y. Ding, I. Ndamukong, Z. Xu, H. Lapko, M. Fromm et al., ATX1-generated H3K4me3 is required for efficient elongation of transcription, not initiation, at ATX1-regulated genes, PLoS Genet, vol.8, p.1003111, 2012.

M. Fromm and Z. Avramova, ATX1/AtCOMPASS and the H3K4me3 marks: how do they activate Arabidopsis genes?, Curr Opin Plant Biol, vol.21, pp.75-82, 2014.

J. Xiao, U. S. Lee, and D. Wagner, Tug of war: adding and removing histone lysine methylation in Arabidopsis, Curr Opin Plant Biol, vol.34, pp.41-53, 2016.

J. C. Fletcher, State of the art: trxG factor regulation of post-embryonic plant development, Front Plant Sci, vol.8, 1925.

Y. Ding, Z. Avramova, and M. Fromm, Two distinct roles of ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1) at promoters and within transcribed regions of ATX1-regulated genes, Plant Cell, vol.23, pp.350-63, 2011.

J. Feng and W. H. Shen, Dynamic regulation and function of histone monoubiquitination in plants, Front Plant Sci, vol.5, p.83, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00959380

D. Jiang, X. Gu, and Y. He, Establishment of the winter-annual growth habit via FRIGIDA-mediated histone methylation at FLOWERING LOCUS C in Arabidopsis, Plant Cell, vol.21, pp.1733-1779, 2009.

D. Jiang, N. C. Kong, X. Gu, Z. Li, and Y. He, Arabidopsis COMPASS-like complexes mediate histone H3 lysine-4 trimethylation to control floral transition and plant development, PLoS Genet, vol.7, p.1001330, 2011.

F. Aquea, A. J. Johnston, P. Canon, U. Grossniklaus, P. Arce-johnson et al., Trithorax-group gene homologue, is required for early embryogenesis in Arabidopsis thaliana, J Exp Bot, vol.61, pp.1215-1239, 2010.

W. C. Liu, Y. H. Li, H. M. Yuan, B. L. Zhang, S. Zhai et al., WD40-REPEAT 5a functions in drought stress tolerance by regulating nitric oxide accumulation in Arabidopsis, Plant Cell Environ, vol.40, pp.543-52, 2017.

Z. T. Song, L. Sun, S. J. Lu, Y. Tian, Y. Ding et al., Transcription factor interaction with COMPASS-like complex regulates histone H3K4 trimethylation for specific gene expression in plants, Proc Natl Acad Sci U S A, vol.112, pp.2900-2905, 2015.

Y. Liu, M. Koornneef, and W. J. Soppe, The absence of histone H2B monoubiquitination in the Arabidopsis hub1 (rdo4) mutant reveals a role for chromatin remodeling in seed dormancy, Plant Cell, vol.19, pp.433-477, 2007.

D. Fleury, K. Himanen, G. Cnops, H. Nelissen, T. M. Boccardi et al., The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth, Plant Cell, vol.19, pp.417-449, 2007.

G. Kapolas, D. Beris, E. Katsareli, P. Livanos, A. Zografidis et al., APRF1 promotes flowering under long days in Arabidopsis thaliana, Plant Sci, vol.253, pp.141-53, 2016.

D. Beris, G. Kapolas, P. Livanos, A. Roussis, D. Milioni et al., RNAimediated silencing of the Arabidopsis thaliana ULCS1 gene, encoding a WDR protein, results in cell wall modification impairment and plant infertility, Plant Sci, vol.245, pp.71-83, 2016.

P. Zimmermann, M. Hirsch-hoffmann, L. Hennig, and G. W. Genevestigator, Arabidopsis microarray database and analysis toolbox, Plant Physiol, vol.136, pp.2621-2653, 2004.

I. Basbouss-serhal, J. Leymarie, and C. Bailly, Fluctuation of Arabidopsis seed dormancy with relative humidity and temperature during dry storage, J Exp Bot, vol.67, pp.119-149, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01373901

J. Leymarie, G. Vitkauskaite, H. H. Hoang, E. Gendreau, V. Chazoule et al., Role of reactive oxygen species in the regulation of Arabidopsis seed dormancy, Plant Cell Physiol, vol.53, pp.96-106, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01560082

Y. Liu, R. Geyer, V. Brambilla, K. Nakabayashi, and W. J. Soppe, Chromatin dynamics during seed dormancy, Methods Mol Biol, vol.773, pp.239-57, 2011.

L. Bentsink, J. Jowett, C. J. Hanhart, and M. Koornneef, Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis, Proc Natl Acad Sci, vol.103, pp.17042-17049, 2006.

R. Yatusevich, H. Fedak, A. Ciesielski, K. Krzyczmonik, A. Kulik et al., Antisense transcription represses Arabidopsis seed dormancy QTL DOG1 to regulate drought tolerance, EMBO Rep, vol.18, pp.2186-96, 2017.

C. Bourbousse, N. Vegesna, and J. A. Law, SOG1 activator and MYB3R repressors regulate a complex DNA damage network in Arabidopsis, Proc Natl Acad Sci U S A, vol.115, pp.12453-62, 2018.

G. Perrella and E. Kaiserli, Light behind the curtain: photoregulation of nuclear architecture and chromatin dynamics in plants, New Phytol, vol.212, pp.908-927, 2016.

C. Bourbousse, I. Ahmed, F. Roudier, G. Zabulon, E. Blondet et al., Histone H2B monoubiquitination facilitates the rapid modulation of gene expression during Arabidopsis photomorphogenesis, PLoS Genet, vol.8, p.1002825, 2012.

F. Li, C. Cheng, F. Cui, M. V. De-oliveira, X. Yu et al., Modulation of RNA polymerase II phosphorylation downstream of pathogen perception orchestrates plant immunity, Cell Host Microbe, vol.16, pp.748-58, 2014.

A. Nassrallah, M. Rougee, C. Bourbousse, S. Drevensek, S. Fonseca et al., DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis, Elife, vol.7, p.37892, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01912108

Y. Cao, Y. Dai, S. Cui, and L. Ma, Histone H2B monoubiquitination in the chromatin of FLOWERING LOCUS C regulates flowering time in Arabidopsis, Plant Cell, vol.20, pp.2586-602, 2008.

X. Gu, D. Jiang, Y. Wang, A. Bachmair, and Y. He, Repression of the floral transition via histone H2B monoubiquitination, Plant J, vol.57, pp.522-555, 2009.

R. J. Schmitz, Y. Tamada, M. R. Doyle, X. Zhang, and R. M. Amasino, Histone H2B deubiquitination is required for transcriptional activation of FLOWERING LOCUS C and for proper control of flowering in Arabidopsis, Plant Physiol, vol.149, pp.1196-204, 2009.

R. Dhawan, H. Luo, A. M. Foerster, S. Abuqamar, H. N. Du et al., HISTONE MONOUBIQUITINATION1 interacts with a subunit of the mediator complex and regulates defense against necrotrophic fungal pathogens in Arabidopsis, Plant Cell, vol.21, pp.1000-1019, 2009.

W. Zhao, P. Neyt, M. Van-lijsebettens, W. H. Shen, and A. Berr, Interactive and noninteractive roles of histone H2B monoubiquitination and H3K36 methylation in the regulation of active gene transcription and control of plant growth and development, New Phytol, vol.221, pp.1101-1117, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01996076

S. Oh, S. Park, and S. Van-nocker, Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis, PLoS Genet, vol.4, p.1000077, 2008.

X. Yao, H. Feng, Y. Yu, A. Dong, and W. H. Shen, SDG2-mediated H3K4 methylation is required for proper Arabidopsis root growth and development, PLoS One, vol.8, p.56537, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00804856

J. Y. Yun, Y. Tamada, Y. E. Kang, and R. M. Amasino, Arabidopsis trithorax-related3/SET domain GROUP2 is required for the winter-annual habit of Arabidopsis thaliana, Plant Cell Physiol, vol.53, pp.834-880, 2012.

A. Tuukkanen, B. Huang, A. Henschel, F. Stewart, and M. Schroeder, Structural modeling of histone methyltransferase complex Set1C from Saccharomyces cerevisiae using constraint-based docking, Proteomics, vol.10, pp.4186-95, 2010.

P. Crevillen and C. Dean, Regulation of the floral repressor gene FLC: the complexity of transcription in a chromatin context, Curr Opin Plant Biol, vol.14, pp.38-44, 2011.

A. Berr, S. Shafiq, and W. H. Shen, Histone modifications in transcriptional activation during plant development, Biochim Biophys Acta, vol.1809, pp.567-76, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00631173

Z. Li, D. Jiang, and Y. He, FRIGIDA establishes a local chromosomal environment for FLOWERING LOCUS C mRNA production, Nat Plants, vol.4, pp.836-882, 2018.

K. Himanen, M. Woloszynska, T. M. Boccardi, S. De-groeve, H. Nelissen et al., Histone H2B monoubiquitination is required to reach maximal transcript levels of circadian clock genes in Arabidopsis, Plant J, vol.72, pp.249-60, 2012.

R. M. Barroco, D. Veylder, L. Magyar, Z. Engler, G. Inze et al., Novel complexes of cyclin-dependent kinases and a cyclin-like protein from Arabidopsis thaliana with a function unrelated to cell division, Cell Mol Life Sci, vol.60, pp.401-413, 2003.

X. Cui, B. Fan, J. Scholz, and Z. Chen, Roles of Arabidopsis cyclin-dependent kinase C complexes in cauliflower mosaic virus infection, plant growth, and development, Plant Cell, vol.19, pp.1388-402, 2007.

Z. W. Wang, Z. Wu, O. Raitskin, Q. Sun, and C. Dean, Antisense-mediated FLC transcriptional repression requires the P-TEFb transcription elongation factor, Proc Natl Acad Sci, vol.111, pp.7468-73, 2014.

K. Fulop, A. Pettko-szandtner, Z. Magyar, P. Miskolczi, E. Kondorosi et al., The Medicago CDKC;1-CYCLINT;1 kinase complex phosphorylates the carboxy-terminal domain of RNA polymerase II and promotes transcription, Plant J, vol.42, pp.810-830, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00019408

W. Antosz, A. Pfab, H. F. Ehrnsberger, P. Holzinger, K. Kollen et al., The composition of the Arabidopsis RNA polymerase II transcript elongation complex reveals the interplay between elongation and mRNA processing factors, Plant Cell, vol.29, pp.854-70, 2017.

R. Alvarez-venegas and Z. Avramova, Methylation patterns of histone H3 Lys 4, Lys 9 and Lys 27 in transcriptionally active and inactive Arabidopsis genes and in atx1 mutants, Nucleic Acids Res, vol.33, pp.5199-207, 2005.

B. Dichtl, R. Aasland, and W. Keller, Functions for S. cerevisiae Swd2p in 3? end formation of specific mRNAs and snoRNAs and global histone 3 lysine 4 methylation, RNA, vol.10, pp.965-77, 2004.

H. Cheng, X. He, and C. Moore, The essential WD repeat protein Swd2 has dual functions in RNA polymerase II transcription termination and lysine 4 methylation of histone H3, Mol Cell Biol, vol.24, pp.2932-2975, 2004.

F. Liu, S. Marquardt, C. Lister, S. Swiezewski, and C. Dean, Targeted 3? processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing, Science, vol.327, pp.94-101, 2010.

A. Roguev, A. Shevchenko, D. Schaft, H. Thomas, A. F. Stewart et al., A comparative analysis of an orthologous proteomic environment in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, Mol Cell Proteomics, vol.3, pp.125-157, 2004.

S. T. Woody, S. Austin-phillips, R. M. Amasino, and P. J. Krysan, The WiscDsLox T-DNA collection: an Arabidopsis community resource generated by using an improved high-throughput T-DNA sequencing pipeline, J Plant Res, vol.120, pp.157-65, 2007.
DOI : 10.1007/s10265-006-0048-x

T. Kuromori, T. Hirayama, Y. Kiyosue, H. Takabe, S. Mizukado et al., A collection of 11 800 single-copy Ds transposon insertion lines in Arabidopsis, Plant J, vol.37, pp.897-905, 2004.

C. A. Schneider, W. S. Rasband, and K. W. Eliceiri, NIH image to ImageJ: 25 years of image analysis, Nat Methods, vol.9, pp.671-676, 2012.

E. Castells, J. Molinier, G. Benvenuto, C. Bourbousse, G. Zabulon et al., The conserved factor DE-ETIOLATED 1 cooperates with CUL4-DDB1DDB2 to maintain genome integrity upon UV stress, EMBO J, vol.30, pp.1162-72, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00580559

P. Poullet, S. Carpentier, and E. Barillot, myProMS, a web server for management and validation of mass spectrometry-based proteomic data, Proteomics, vol.7, pp.2553-2559, 2007.

Y. Wang, X. J. Hu, X. D. Zou, X. H. Wu, Z. Q. Ye et al., WDSPdb: a database for WD40-repeat proteins, Nucleic Acids Res, vol.43, pp.339-383, 2015.

Y. Wang, F. Jiang, Z. Zhuo, X. H. Wu, and Y. D. Wu, A method for WD40 repeat detection and secondary structure prediction, PLoS One, vol.8, p.65705, 2013.
DOI : 10.1371/journal.pone.0065705

URL : https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0065705&type=printable

S. Chang, J. Puryear, and J. Cairney, A simple and efficient method for isolating RNA from pine trees, Plant Mol Biol Report, vol.11, pp.113-119, 1993.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2134, 2014.
DOI : 10.1093/bioinformatics/btu170

URL : https://academic.oup.com/bioinformatics/article-pdf/30/15/2114/17143152/btu170.pdf

C. Y. Cheng, V. Krishnakumar, A. P. Chan, F. Thibaud-nissen, S. Schobel et al., Araport11: a complete reannotation of the Arabidopsis thaliana reference genome, Plant J, vol.89, pp.789-804, 2017.

A. Dobin, C. A. Davis, F. Schlesinger, J. Drenkow, C. Zaleski et al., STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, pp.15-21, 2013.
DOI : 10.1093/bioinformatics/bts635

URL : https://academic.oup.com/bioinformatics/article-pdf/29/1/15/17101697/bts635.pdf

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat Methods, vol.9, pp.357-366, 2012.
DOI : 10.1038/nmeth.1923

URL : http://europepmc.org/articles/pmc3322381?pdf=render

Y. Zhang, T. Liu, C. A. Meyer, J. Eeckhoute, D. S. Johnson et al., Model-based analysis of ChIP-Seq (MACS)

, Genome Biol, vol.9, p.137, 2008.

A. R. Quinlan and I. M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, pp.841-843, 2010.

F. Ramirez, D. P. Ryan, B. Gruning, V. Bhardwaj, F. Kilpert et al., deepTools2: a next generation web server for deepsequencing data analysis, Nucleic Acids Res, vol.44, pp.160-165, 2016.

E. I. Boyle, S. Weng, J. Gollub, H. Jin, D. Botstein et al., GO:: TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes, Bioinformatics, vol.20, pp.3710-3715, 2004.

F. Supek, M. Bosnjak, N. Skunca, and T. Smuc, REVIGO summarizes and visualizes long lists of gene ontology terms, PLoS One, vol.6, p.21800, 2011.

D. Loew and G. Arras, SDG2 and S2Lb affinity purification and mass spectrometry, 2019.

L. Concia, ChIP-seq and RNA-seq in HUB1 and SWD2 Arabidopsis mutant seedlings, 2019.

A. Veluchamy, RNAPol-II. Gene expression omnibus, 2016.

A. Veluchamy, RNAPol-II, Gene Expression omnibus, 2016.